FMO DATABASE

FMODB ID: 7M28K

Calculation Name: 1BKB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1BKB

Chain ID: A

ChEMBL ID:

UniProt ID: P56635

Base Structure: X-ray

Registration Date: 2023-09-27

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1122354.422675
FMO2-HF: Nuclear repulsion	1069328.183857
FMO2-HF: Total energy	-53026.238818
FMO2-MP2: Total energy	-53180.478095

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:4:LYS)

Summations of interaction energy for fragment #1(A:4:LYS)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-84.108	-78.745	1.765	-3.014	-4.116	-0.015

Interaction energy analysis for fragmet #1(A:4:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.996 / q_NPA : 1.003

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	6	VAL	0	-0.015	-0.020	2.389	-17.361	-12.244	1.767	-2.961	-3.924	-0.015
4	A	7	MET	0	0.030	0.014	4.584	4.622	4.768	-0.001	-0.023	-0.123	0.000
5	A	8	SER	0	-0.016	-0.006	8.388	-1.067	-1.067	0.000	0.000	0.000	0.000
6	A	9	THR	0	-0.010	-0.006	11.368	-0.083	-0.083	0.000	0.000	0.000	0.000
7	A	10	LYS	1	0.958	0.990	13.258	17.344	17.344	0.000	0.000	0.000	0.000
8	A	11	TYR	0	-0.001	-0.014	15.591	-0.288	-0.288	0.000	0.000	0.000	0.000
9	A	12	VAL	0	-0.027	-0.003	19.747	0.222	0.222	0.000	0.000	0.000	0.000
10	A	13	GLU	-1	-0.867	-0.936	23.392	-11.257	-11.257	0.000	0.000	0.000	0.000
11	A	14	ALA	0	0.016	0.004	26.418	0.109	0.109	0.000	0.000	0.000	0.000
12	A	15	GLY	0	-0.076	-0.056	27.400	0.211	0.211	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.910	-0.948	26.772	-11.459	-11.459	0.000	0.000	0.000	0.000
14	A	17	LEU	0	-0.062	-0.012	24.106	-0.059	-0.059	0.000	0.000	0.000	0.000
15	A	18	LYS	1	0.930	0.939	27.980	10.532	10.532	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.906	-0.944	28.687	-9.984	-9.984	0.000	0.000	0.000	0.000
17	A	20	GLY	0	-0.028	-0.018	27.784	0.126	0.126	0.000	0.000	0.000	0.000
18	A	21	SER	0	-0.050	-0.024	25.028	-0.392	-0.392	0.000	0.000	0.000	0.000
19	A	22	TYR	0	0.014	-0.008	20.102	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	23	VAL	0	0.036	0.004	20.209	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.008	0.001	14.771	-0.034	-0.034	0.000	0.000	0.000	0.000
22	A	25	ILE	0	-0.046	-0.015	17.971	0.542	0.542	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.899	-0.959	18.209	-15.359	-15.359	0.000	0.000	0.000	0.000
24	A	27	GLY	0	-0.009	-0.003	14.173	-0.272	-0.272	0.000	0.000	0.000	0.000
25	A	28	GLU	-1	-0.749	-0.873	13.907	-20.698	-20.698	0.000	0.000	0.000	0.000
26	A	29	PRO	0	-0.032	0.011	14.331	0.888	0.888	0.000	0.000	0.000	0.000
27	A	30	CYS	0	-0.047	-0.026	17.038	0.599	0.599	0.000	0.000	0.000	0.000
28	A	31	ARG	1	0.970	0.995	20.825	12.240	12.240	0.000	0.000	0.000	0.000
29	A	32	VAL	0	-0.020	-0.021	23.816	0.313	0.313	0.000	0.000	0.000	0.000
30	A	33	VAL	0	-0.035	-0.031	26.641	0.186	0.186	0.000	0.000	0.000	0.000
31	A	34	GLU	-1	-0.837	-0.925	29.860	-9.263	-9.263	0.000	0.000	0.000	0.000
32	A	35	ILE	0	-0.029	-0.009	29.512	-0.332	-0.332	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.878	-0.906	32.560	-8.544	-8.544	0.000	0.000	0.000	0.000
34	A	37	LYS	1	0.916	0.958	32.330	9.554	9.554	0.000	0.000	0.000	0.000
35	A	38	SER	0	0.042	0.024	36.670	0.240	0.240	0.000	0.000	0.000	0.000
36	A	39	LYS	1	0.949	0.965	38.167	7.522	7.522	0.000	0.000	0.000	0.000
37	A	40	THR	0	0.027	0.027	39.732	0.158	0.158	0.000	0.000	0.000	0.000
38	A	41	GLY	0	0.022	0.023	40.423	0.187	0.187	0.000	0.000	0.000	0.000
39	A	42	LYS	1	0.983	0.985	41.675	6.371	6.371	0.000	0.000	0.000	0.000
40	A	43	HIS	0	0.009	-0.009	42.547	-0.026	-0.026	0.000	0.000	0.000	0.000
41	A	44	GLY	0	-0.002	0.010	38.663	-0.113	-0.113	0.000	0.000	0.000	0.000
42	A	45	SER	0	0.077	0.041	33.336	0.147	0.147	0.000	0.000	0.000	0.000
43	A	46	ALA	0	-0.012	-0.006	36.280	0.091	0.091	0.000	0.000	0.000	0.000
44	A	47	LYS	1	0.859	0.925	32.929	8.907	8.907	0.000	0.000	0.000	0.000
45	A	48	ALA	0	0.024	0.001	30.603	0.258	0.258	0.000	0.000	0.000	0.000
46	A	49	ARG	1	0.894	0.947	31.051	9.244	9.244	0.000	0.000	0.000	0.000
47	A	50	ILE	0	0.003	-0.005	25.970	0.221	0.221	0.000	0.000	0.000	0.000
48	A	51	VAL	0	-0.007	0.003	28.411	-0.178	-0.178	0.000	0.000	0.000	0.000
49	A	52	ALA	0	0.015	0.000	24.243	0.062	0.062	0.000	0.000	0.000	0.000
50	A	53	VAL	0	-0.012	-0.008	24.646	0.207	0.207	0.000	0.000	0.000	0.000
51	A	54	GLY	0	0.046	0.021	20.547	-0.381	-0.381	0.000	0.000	0.000	0.000
52	A	55	VAL	0	-0.044	-0.031	18.103	0.526	0.526	0.000	0.000	0.000	0.000
53	A	56	PHE	0	-0.024	-0.029	14.271	0.080	0.080	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.807	-0.873	18.449	-15.242	-15.242	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.014	0.022	20.561	0.654	0.654	0.000	0.000	0.000	0.000
56	A	59	GLY	0	-0.017	-0.001	22.601	0.691	0.691	0.000	0.000	0.000	0.000
57	A	60	LYS	1	0.872	0.942	24.067	9.930	9.930	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.870	0.909	19.209	15.637	15.637	0.000	0.000	0.000	0.000
59	A	62	THR	0	-0.014	-0.022	25.319	0.461	0.461	0.000	0.000	0.000	0.000
60	A	63	LEU	0	0.030	0.018	23.091	-0.243	-0.243	0.000	0.000	0.000	0.000
61	A	64	SER	0	-0.003	-0.002	26.838	0.449	0.449	0.000	0.000	0.000	0.000
62	A	65	LEU	0	-0.009	0.006	25.392	-0.094	-0.094	0.000	0.000	0.000	0.000
63	A	66	PRO	0	-0.013	-0.018	28.487	0.301	0.301	0.000	0.000	0.000	0.000
64	A	67	VAL	0	-0.020	-0.021	29.488	-0.307	-0.307	0.000	0.000	0.000	0.000
65	A	68	ASP	-1	-0.845	-0.915	29.747	-10.363	-10.363	0.000	0.000	0.000	0.000
66	A	69	ALA	0	-0.040	-0.005	25.650	-0.246	-0.246	0.000	0.000	0.000	0.000
67	A	70	GLN	0	0.003	-0.008	20.251	-0.087	-0.087	0.000	0.000	0.000	0.000
68	A	71	VAL	0	-0.013	-0.004	21.537	-0.110	-0.110	0.000	0.000	0.000	0.000
69	A	72	GLU	-1	-0.852	-0.925	13.537	-23.043	-23.043	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.046	-0.017	17.662	0.523	0.523	0.000	0.000	0.000	0.000
71	A	74	PRO	0	-0.020	0.000	14.758	-0.954	-0.954	0.000	0.000	0.000	0.000
72	A	75	ILE	0	-0.017	-0.015	12.833	1.415	1.415	0.000	0.000	0.000	0.000
73	A	76	ILE	0	-0.035	-0.025	13.871	-1.182	-1.182	0.000	0.000	0.000	0.000
74	A	77	GLU	-1	-0.866	-0.893	13.834	-21.223	-21.223	0.000	0.000	0.000	0.000
75	A	78	LYS	1	0.841	0.917	16.026	13.699	13.699	0.000	0.000	0.000	0.000
76	A	79	PHE	0	-0.016	-0.008	15.370	0.113	0.113	0.000	0.000	0.000	0.000
77	A	80	THR	0	0.013	0.008	19.884	0.125	0.125	0.000	0.000	0.000	0.000
78	A	81	ALA	0	0.001	0.003	19.860	-0.442	-0.442	0.000	0.000	0.000	0.000
79	A	82	GLN	0	0.048	0.023	21.940	0.605	0.605	0.000	0.000	0.000	0.000
80	A	83	ILE	0	-0.035	-0.014	23.542	-0.511	-0.511	0.000	0.000	0.000	0.000
81	A	84	LEU	0	-0.019	-0.003	21.920	0.591	0.591	0.000	0.000	0.000	0.000
82	A	85	SER	0	-0.036	-0.032	24.819	0.497	0.497	0.000	0.000	0.000	0.000
83	A	86	VAL	0	0.014	0.005	24.893	-0.525	-0.525	0.000	0.000	0.000	0.000
84	A	87	SER	0	-0.001	0.013	24.555	0.396	0.396	0.000	0.000	0.000	0.000
85	A	88	GLY	0	0.012	-0.006	26.802	-0.028	-0.028	0.000	0.000	0.000	0.000
86	A	89	ASP	-1	-0.903	-0.953	23.203	-12.508	-12.508	0.000	0.000	0.000	0.000
87	A	90	VAL	0	-0.039	-0.022	19.423	-0.791	-0.791	0.000	0.000	0.000	0.000
88	A	91	ILE	0	-0.003	0.004	20.934	0.792	0.792	0.000	0.000	0.000	0.000
89	A	92	GLN	0	-0.002	0.007	20.123	-0.332	-0.332	0.000	0.000	0.000	0.000
90	A	93	LEU	0	-0.010	-0.012	18.486	0.819	0.819	0.000	0.000	0.000	0.000
91	A	94	MET	0	0.038	0.023	19.564	-0.561	-0.561	0.000	0.000	0.000	0.000
92	A	95	ASP	-1	-0.748	-0.865	16.056	-18.071	-18.071	0.000	0.000	0.000	0.000
93	A	96	MET	0	-0.020	-0.002	19.069	0.108	0.108	0.000	0.000	0.000	0.000
94	A	97	ARG	1	0.747	0.846	14.299	20.033	20.033	0.000	0.000	0.000	0.000
95	A	98	ASP	-1	-0.798	-0.901	15.496	-19.298	-19.298	0.000	0.000	0.000	0.000
96	A	99	TYR	0	-0.031	-0.018	19.137	0.248	0.248	0.000	0.000	0.000	0.000
97	A	100	LYS	1	0.784	0.893	12.554	21.330	21.330	0.000	0.000	0.000	0.000
98	A	101	THR	0	-0.020	-0.020	17.466	0.639	0.639	0.000	0.000	0.000	0.000
99	A	102	ILE	0	-0.043	-0.013	13.551	-1.233	-1.233	0.000	0.000	0.000	0.000
100	A	103	GLU	-1	-0.887	-0.936	15.126	-15.384	-15.384	0.000	0.000	0.000	0.000
101	A	104	VAL	0	-0.021	-0.014	15.400	-1.359	-1.359	0.000	0.000	0.000	0.000
102	A	105	PRO	0	0.000	0.009	16.185	0.974	0.974	0.000	0.000	0.000	0.000
103	A	106	MET	0	0.067	0.016	19.175	0.009	0.009	0.000	0.000	0.000	0.000
104	A	107	LYS	1	0.905	0.967	17.021	17.951	17.951	0.000	0.000	0.000	0.000
105	A	108	TYR	0	-0.058	-0.037	14.882	-0.587	-0.587	0.000	0.000	0.000	0.000
106	A	109	VAL	0	0.032	0.013	19.966	-0.374	-0.374	0.000	0.000	0.000	0.000
107	A	110	GLU	-1	-0.818	-0.899	22.924	-13.186	-13.186	0.000	0.000	0.000	0.000
108	A	111	GLU	-1	-0.794	-0.894	25.248	-11.290	-11.290	0.000	0.000	0.000	0.000
109	A	112	GLU	-1	-0.928	-0.969	28.490	-10.655	-10.655	0.000	0.000	0.000	0.000
110	A	113	ALA	0	-0.079	-0.040	26.512	0.301	0.301	0.000	0.000	0.000	0.000
111	A	114	LYS	1	0.851	0.910	25.577	12.101	12.101	0.000	0.000	0.000	0.000
112	A	115	GLY	0	-0.007	0.007	28.824	0.142	0.142	0.000	0.000	0.000	0.000
113	A	116	ARG	1	0.874	0.930	30.985	9.873	9.873	0.000	0.000	0.000	0.000
114	A	117	LEU	0	-0.002	0.025	25.353	-0.113	-0.113	0.000	0.000	0.000	0.000
115	A	118	ALA	0	0.018	-0.001	29.138	0.267	0.267	0.000	0.000	0.000	0.000
116	A	119	PRO	0	0.010	0.004	28.581	-0.244	-0.244	0.000	0.000	0.000	0.000
117	A	120	GLY	0	-0.018	-0.011	28.527	0.404	0.404	0.000	0.000	0.000	0.000
118	A	121	ALA	0	-0.058	-0.017	28.989	0.094	0.094	0.000	0.000	0.000	0.000
119	A	122	GLU	-1	-0.879	-0.932	26.349	-11.726	-11.726	0.000	0.000	0.000	0.000
120	A	123	VAL	0	0.013	0.005	22.508	0.389	0.389	0.000	0.000	0.000	0.000
121	A	124	GLU	-1	-0.818	-0.884	22.398	-13.360	-13.360	0.000	0.000	0.000	0.000
122	A	125	VAL	0	-0.021	-0.018	16.958	-0.015	-0.015	0.000	0.000	0.000	0.000
123	A	126	TRP	0	-0.064	-0.056	17.385	0.035	0.035	0.000	0.000	0.000	0.000
124	A	127	GLN	0	0.047	0.024	8.901	1.930	1.930	0.000	0.000	0.000	0.000
125	A	128	ILE	0	-0.021	-0.015	12.174	0.545	0.545	0.000	0.000	0.000	0.000
126	A	129	LEU	0	0.001	-0.004	7.106	-0.506	-0.506	0.000	0.000	0.000	0.000
127	A	130	ASP	-1	-0.915	-0.949	4.366	-60.771	-60.671	-0.001	-0.030	-0.069	0.000
128	A	131	ARG	1	0.813	0.914	7.558	25.831	25.831	0.000	0.000	0.000	0.000
129	A	132	TYR	0	0.010	-0.016	10.939	0.274	0.274	0.000	0.000	0.000	0.000
130	A	133	LYS	1	0.780	0.881	14.418	15.094	15.094	0.000	0.000	0.000	0.000
131	A	134	ILE	0	0.008	0.020	18.013	0.143	0.143	0.000	0.000	0.000	0.000
132	A	135	ILE	0	0.011	-0.003	20.696	0.466	0.466	0.000	0.000	0.000	0.000
133	A	136	ARG	1	0.954	0.971	23.513	11.824	11.824	0.000	0.000	0.000	0.000
134	A	137	VAL	0	0.007	-0.002	26.056	-0.248	-0.248	0.000	0.000	0.000	0.000
135	A	138	LYS	1	0.838	0.899	27.940	9.949	9.949	0.000	0.000	0.000	0.000
136	A	139	GLY	0	0.074	0.052	26.040	-0.081	-0.081	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:LYS)